bims-lysosi 2022-01-23 papers

bims-lysosi

Biomed News

on Lysosomes and signaling

Issue of 2022–01–23
thirty-two papers selected by
Stephanie Fernandes, Max Planck Institute for Biology of Ageing

Lysosome-Targeting Strategy Using Polypeptides and Chimeric Molecules.
Lysosomal dysfunction in neurodegeneration: emerging concepts and methods.
Renal cell carcinoma associated with tuberous sclerosis complex (TSC)/mammalian target of rapamycin (MTOR) genetic alterations.
Large-Scale, Wavelet-Based Analysis of Lysosomal Trajectories and Co-Movements of Lysosomes with Nanoparticle Cargos.
Neuroinflammation in aucher disease, neuronal ceroid lipofuscinosis, and commonalities with Parkinson's disease.
Neutral Sphingomyelinase 2 controls exosomes secretion via counteracting V-ATPase-mediated endosome acidification.
Intravitreal gene therapy restores the autophagy-lysosomal pathway and attenuates retinal degeneration in cathepsin D-deficient mice.
Endolysosomal Cation Channels and Lung Disease.
The ins and outs of virus trafficking through acidic Ca2+ stores.
TFEB Regulates ATP7B Expression to Promote Platinum Chemoresistance in Human Ovarian Cancer Cells.
The Lysosomal Rag-Ragulator Complex Licenses RIPK1 and Caspase-8-mediated Pyroptosis by Yersinia.
Adipocyte-Specific Inhibition of Mir221/222 Ameliorates Diet-Induced Obesity Through Targeting Ddit4.
Sensing of RNA stress by mTORC1 drives autoinflammation.
Progranulin as a therapeutic target in neurodegenerative diseases.
ARF GTPases activate Salmonella effector SopF to ADP-ribosylate host V-ATPase and inhibit endomembrane damage-induced autophagy.
Tfeb-Mediated Transcriptional Regulation of Autophagy Induces Autosis during Ischemia/Reperfusion in the Heart.
Renal mTORC1 activation is associated with disease activity and prognosis in lupus nephritis.
The Cerebellum in Niemann-Pick C1 Disease: Mouse Versus Man.
Selective elimination of pluripotent stem cells by PIKfyve specific inhibitors.
Selective Deletion of the Mechanistic Target of Rapamycin From the Renal Collecting Duct Principal Cell in Mice Down-Regulates the Epithelial Sodium Channel.
TFEB signaling attenuates NLRP3-driven inflammatory responses in severe asthma.
Role of Branched-chain Amino Acid Metabolism in Tumor Development and Progression.
An endosome-associated actin network involved in directed apical plasma membrane growth.
Amino Acid Sensing and Assimilation by the Fungal Pathogen Candida albicans in the Human Host.
Lipid kinases VPS34 and PIKfyve coordinate a phosphoinositide cascade to regulate Retriever-mediated recycling on endosomes.
mTORC2 forms iron-clad defense to guard memory.
Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.
Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis.
Cytoplasmic RNA quality control failure engages mTORC1-mediated autoinflammatory disease.
Nephropathic Cystinosis: Pathogenic Roles of Inflammation and Potential for New Therapies.
Subcutaneous nanotherapy repurposes the immunosuppressive mechanism of rapamycin to enhance allogeneic islet graft viability.
Yeast has evolved to minimize protein resource cost for synthesizing amino acids.

ACS Omega. 2022 Jan 11. 7(1): 5-16

Lysosome-Targeting Strategy Using Polypeptides and Chimeric Molecules.

Basudeb Mondal, Tahiti Dutta, Abinash Padhy, Sabyasachi Das, Sayam Sen Gupta.

Lysosomes are membranous compartments containing hydrolytic enzymes, where cellular degradation of proteins and enzymes among others occurs in a controlled manner. Lysosomal dysfunction results in various pathological situations, such as several lysosomal storage disorders, neurodegeneration, infectious diseases, cancers, and aging. In this review, we have discussed different strategies for synthesizing peptides/chimeric molecules, their lysosome-targeting ability, and their ability to treat several lysosomal associated diseases, including lysosomal storage diseases and cancers. We have also discussed the delivery of cargo molecules into the lysosome using lysosome-targeting ligand-decorated nanocarriers. The introduction of a protein-binding ligand along with a lysosome-targeting ligand to manufacture a chimeric architecture for cell-specific protein (extracellular and membrane protein) degradation ability has been discussed thoroughly. Finally, the future applications of these lysosome-targeting peptides, nanocarriers, and chimeric molecules have been pointed out.

DOI: https://doi.org/10.1021/acsomega.1c04771
Trends Neurosci. 2022 Jan 13. pii: S0166-2236(21)00252-6. [Epub ahead of print]

Lysosomal dysfunction in neurodegeneration: emerging concepts and methods.

Vinod Udayar, Yu Chen, Ellen Sidransky, Ravi Jagasia.

  The understanding of lysosomes has come a long way since the initial discovery of their role in degrading cellular waste. The lysosome is now recognized as a highly dynamic organelle positioned at the crossroads of cell signaling, transcription, and metabolism. Underscoring its importance is the observation that, in addition to rare monogenic lysosomal storage disorders, genes regulating lysosomal function are implicated in common sporadic neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). Developing therapies for these disorders is particularly challenging, largely due to gaps in knowledge of the underlying molecular and cellular processes. In this review, we discuss technological advances that have propelled deeper understanding of the lysosome in neurodegeneration, from elucidating the functions of lysosome-related disease risk variants at the level of the organelle, cell, and tissue, to the development of disease-specific biological models that recapitulate disease manifestations. Finally, we identify key questions to be addressed to successfully bridge the gap to the clinic.

Keywords:  Alzheimer’s disease; Parkinson’s disease; amyotrophic lateral sclerosis; frontotemporal dementia; lysosomes

DOI:  https://doi.org/10.1016/j.tins.2021.12.004
Mod Pathol. 2022 Jan 19.

Renal cell carcinoma associated with tuberous sclerosis complex (TSC)/mammalian target of rapamycin (MTOR) genetic alterations.

Pedram Argani, Rohit Mehra.

DOI: https://doi.org/10.1038/s41379-021-00971-y
Cells. 2022 Jan 13. pii: 270. [Epub ahead of print]11(2):

Large-Scale, Wavelet-Based Analysis of Lysosomal Trajectories and Co-Movements of Lysosomes with Nanoparticle Cargos.

Konstantin Polev, Diana V Kolygina, Kristiana Kandere-Grzybowska, Bartosz A Grzybowski.

  Lysosomes-that is, acidic organelles known for degradation/recycling-move through the cytoplasm alternating between bursts of active transport and short, diffusive motions or even pauses. While their mobility is essential for lysosomes' fusogenic and non-fusogenic interactions with target organelles, their movements have not been characterized in adequate detail. Here, large-scale statistical analysis of lysosomal movement trajectories reveals that lysosome trajectories in all examined cell types-both cancer and noncancerous ones-are superdiffusive and characterized by heavy-tailed distributions of run and flight lengths. Consideration of Akaike weights for various potential models (lognormal, power law, truncated power law, stretched exponential, and exponential) indicates that the experimental data are best described by the lognormal distribution, which, in turn, can be related to one of the space-search strategies particularly effective when "thorough" search needs to balance search for rare target(s) (organelles). In addition, automated, wavelet-based analysis allows for co-tracking the motions of lysosomes and the cargos they carry-particularly the nanoparticle aggregates known to cause selective lysosome disruption in cancerous cells. The methods we describe here could help study nanoparticle assemblies, viruses, and other objects transported inside various vesicle types, as well as coordinated movements of organelles/particles in the cytoplasm. Custom-written code that includes integrated workflow for our analyses is made available for academic use.

Keywords:  cancer lysosomes; confocal reflection microscopy; continuous wavelet transform; lognormal distribution; lysosome transport; lysosome-nanoparticle co-movement; maximum-likelihood estimates; mixed-charge nanoparticles

DOI:  https://doi.org/10.3390/cells11020270
Brain Res. 2022 Jan 18. pii: S0006-8993(22)00022-1. [Epub ahead of print] 147798

Neuroinflammation in aucher disease, neuronal ceroid lipofuscinosis, and commonalities with Parkinson's disease.

Laetitia Francelle, Joseph R Mazzulli.

  Lysosomal storage diseases (LSDs) are rare genetic disorders caused by a disruption in cellular clearance, resulting in pathological storage of undegraded lysosomal substrates. Recent clinical and genetic studies have uncovered links between multiple LSDs and common neurodegenerative diseases such as Parkinson's disease (PD). Here, we review recent literature describing the role of glia cells and neuroinflammation in PD and LSDs, including Gaucher disease (GD) and neuronal ceroid lipofuscinosis (NCL), and highlight converging inflammation pathways that lead to neuron loss. Recent data indicates that lysosomal dysfunction and accumulation of storage materials can initiate the activation of glial cells, through interaction with cell surface or cytosolic pattern recognition receptors that detect pathogenic aggregates of cellular debris. Activated glia cells could act to protect neurons through the elimination of toxic protein or lipid aggregates early in the disease process. However prolonged glial activation that occurs over several decades in chronic-age related neurodegeneration could induce the inappropriate elimination of synapses, leading to neuron loss. These studies provide mechanistic insight into the relationship between lysosomal dysfunction and glial activation, and offer novel therapeutic pathways for the treatment of PD and LSDs focused on reducing neuroinflammation and mitigating cell loss.

Keywords:  Batten’s disease; Gaucher Disease; Neuroinflammation; Parkinson’s disease; lysosomal storage disorders

DOI:  https://doi.org/10.1016/j.brainres.2022.147798
J Cell Sci. 2022 Jan 20. pii: jcs.259324. [Epub ahead of print]

Neutral Sphingomyelinase 2 controls exosomes secretion via counteracting V-ATPase-mediated endosome acidification.

Dolma Choezom, Julia Christina Gross.

  During endosome maturation, neutral sphingomyelinase 2 (nSMase2) is involved in intraluminal vesicles (ILVs) budding into late endosomes or multivesicular bodies (MVBs). Fusion of these with the plasma membrane results in exosomes or small extracellular vesicles (sEV) secretion. Here, we describe nSMase2 activity to control sEV secretion through modulation of V-ATPase activity. Specifically, we show that nSMase2 inhibition induces V-ATPase complex assembly that drives MVB lumen acidification and consequently reduces sEV secretion. Conversely, we further demonstrate that stimulating nSMase2 activity with the inflammatory cytokine TNFα decreases acidification and increases sEV secretion. Thus, we find that nSMase2 activity affects MVB membrane lipid composition to counteract V-ATPase-mediated endosome acidification, thereby shifting MVB fate towards sEV secretion.

Keywords:  Endosomal cargo sorting; Endosomal maturation; Intraluminal vesicles; Secretory Multivesicular Bodies; Small extracellular vesicles

DOI:  https://doi.org/10.1242/jcs.259324
Neurobiol Dis. 2022 Jan 13. pii: S0969-9961(22)00019-5. [Epub ahead of print]164 105628

Intravitreal gene therapy restores the autophagy-lysosomal pathway and attenuates retinal degeneration in cathepsin D-deficient mice.

Junling Liu, Mahmoud Bassal, Stefanie Schlichting, Ingke Braren, Alessandro Di Spiezio, Paul Saftig, Udo Bartsch.

  Loss of vision due to progressive retinal degeneration is a hallmark of neuronal ceroid lipofuscinoses (NCL), a group of fatal neurodegenerative lysosomal storage diseases. Enzyme substitution therapies represent promising treatment options for NCLs caused by dysfunctions of soluble lysosomal enzymes. Here, we compared the efficacy of a cell-based enzyme substitution strategy and a gene therapy approach to attenuate the retinal pathology in cathepsin D- (CTSD) deficient mice, an animal model of CLN10 disease. Levels of enzymatically active CTSD in mutant retinas were significantly higher after an adeno-associated virus vector-mediated CTSD transfer to retinal glial cells and retinal pigment epithelial cells than after intravitreal transplantations of a CTSD overexpressing clonal neural stem cell line. In line with this finding, the gene therapy treatment restored the disrupted autophagy-lysosomal pathway more effectively than the cell-based approach, as indicated by a complete clearance of storage, significant attenuation of lysosomal hypertrophy, and normalized levels of the autophagy marker sequestosome 1/p62 and microtubule-associated protein 1 light chain 3-II. While the cell-based treatment did not prevent the rapidly progressing loss of various retinal cell types, the gene therapy approach markedly attenuated retinal degeneration as demonstrated by a pronounced rescue of photoreceptor cells and rod bipolar cells.

Keywords:  Autophagy; CLN10 disease; Cathepsin D; Enzyme replacement therapy; Gene therapy; Lysosome; Neural stem cells; Neuronal ceroid lipofuscinosis; Retinal degeneration

DOI:  https://doi.org/10.1016/j.nbd.2022.105628
Cells. 2022 Jan 17. pii: 304. [Epub ahead of print]11(2):

Endolysosomal Cation Channels and Lung Disease.

Barbara Spix, Aicha Jeridi, Meshal Ansari, Ali Önder Yildirim, Herbert B Schiller, Christian Grimm.

  Endolysosomal cation channels are emerging as key players of endolysosomal function such as endolysosomal trafficking, fusion/fission, lysosomal pH regulation, autophagy, lysosomal exocytosis, and endocytosis. Diseases comprise lysosomal storage disorders (LSDs) and neurodegenerative diseases, metabolic diseases, pigmentation defects, cancer, immune disorders, autophagy related diseases, infectious diseases and many more. Involvement in lung diseases has not been a focus of attention so far but recent developments in the field suggest critical functions in lung physiology and pathophysiology. Thus, loss of TRPML3 was discovered to exacerbate emphysema formation and cigarette smoke induced COPD due to dysregulated matrix metalloproteinase 12 (MMP-12) levels in the extracellular matrix of the lung, a known risk factor for emphysema/COPD. While direct lung function measurements with the exception of TRPML3 are missing for other endolysosomal cation channels or channels expressed in lysosome related organelles (LRO) in the lung, links between those channels and important roles in lung physiology have been established such as the role of P2X4 in surfactant release from alveolar epithelial Type II cells. Other channels with demonstrated functions and disease relevance in the lung such as TRPM2, TRPV2, or TRPA1 may mediate their effects due to plasma membrane expression but evidence accumulates that these channels might also be expressed in endolysosomes, suggesting additional and/or dual roles of these channels in cell and intracellular membranes. We will discuss here the current knowledge on cation channels residing in endolysosomes or LROs with respect to their emerging roles in lung disease.

Keywords:  BK; COPD; TRPA1; TRPM2; TRPML; TRPML3; TRPV2; asthma; cystic fibrosis; emphysema; lung injury

DOI:  https://doi.org/10.3390/cells11020304
Cell Calcium. 2022 Jan 06. pii: S0143-4160(22)00003-3. [Epub ahead of print]102 102528

The ins and outs of virus trafficking through acidic Ca2+ stores.

Gihan S Gunaratne, Jonathan S Marchant.

  Many viruses exploit host-cell Ca2+ signaling processes throughout their life cycle. This is especially relevant for viruses that translocate through the endolysosomal system, where cellular infection is keyed to the microenvironment of these acidic Ca2+ stores and Ca2+-dependent trafficking pathways. As regulators of the endolysosomal ionic milieu and trafficking dynamics, two families of endolysosomal Ca2+-permeable cation channels - two pore channels (TPCs) and transient receptor potential mucolipins (TRPMLs) - have emerged as important host-cell factors in viral entry. Here, we review: (i) current evidence implicating Ca2+ signaling in viral translocation through the endolysosomal system, (ii) the roles of these ion channels in supporting cellular infection by different viruses, and (iii) areas for future research that will help define the potential of TPC and TRPML ligands as progressible antiviral agents.

Keywords:  Coronavirus; Endosomes; Lysosomes; Mucolipins; NAADP; Two-pore channel

DOI:  https://doi.org/10.1016/j.ceca.2022.102528
Cells. 2022 Jan 10. pii: 219. [Epub ahead of print]11(2):

TFEB Regulates ATP7B Expression to Promote Platinum Chemoresistance in Human Ovarian Cancer Cells.

Raffaella Petruzzelli, Marta Mariniello, Rossella De Cegli, Federico Catalano, Floriana Guida, Elia Di Schiavi, Roman S Polishchuk.

  ATP7B is a hepato-specific Golgi-located ATPase, which plays a key role in the regulation of copper (Cu) homeostasis and signaling. In response to elevated Cu levels, ATP7B traffics from the Golgi to endo-lysosomal structures, where it sequesters excess copper and further promotes its excretion to the bile at the apical surface of hepatocytes. In addition to liver, high ATP7B expression has been reported in tumors with elevated resistance to platinum (Pt)-based chemotherapy. Chemoresistance to Pt drugs represents the current major obstacle for the treatment of large cohorts of cancer patients. Although the mechanisms underlying Pt-tolerance are still ambiguous, accumulating evidence suggests that lysosomal sequestration of Pt drugs by ion transporters (including ATP7B) might significantly contribute to drug resistance development. In this context, signaling mechanisms regulating the expression of transporters such as ATP7B are of great importance. Considering this notion, we investigated whether ATP7B expression in Pt-resistant cells might be driven by transcription factor EB (TFEB), a master regulator of lysosomal gene transcription. Using resistant ovarian cancer IGROV-CP20 cells, we found that TFEB directly binds to the predicted coordinated lysosomal expression and regulation (CLEAR) sites in the proximal promoter and first intron region of ATP7B upon Pt exposure. This binding accelerates transcription of luciferase reporters containing ATP7B CLEAR regions, while suppression of TFEB inhibits ATP7B expression and stimulates cisplatin toxicity in resistant cells. Thus, these data have uncovered a Pt-dependent transcriptional mechanism that contributes to cancer chemoresistance and might be further explored for therapeutic purposes.

Keywords:  ATP7B; Golgi; TFEB; chemoresistance; ovarian cancer

DOI:  https://doi.org/10.3390/cells11020219
Science. 2021 Jun 25. pii: eabg0269. [Epub ahead of print]372(6549):

The Lysosomal Rag-Ragulator Complex Licenses RIPK1 and Caspase-8-mediated Pyroptosis by Yersinia.

Zengzhang Zheng, Wanyan Deng, Yang Bai, Rui Miao, Shenglin Mei, Zhibin Zhang, Youdong Pan, Yi Wang, Rui Min, Fan Deng, Zeyu Wu, Wu Li, Pengcheng Chen, Tianchi Ma, Xiwen Lou, Judy Lieberman, Xing Liu.

Host cells initiate cell death programs to limit pathogen infection. Inhibition of transforming growth factor-β-activated kinase 1 (TAK1) by pathogenic Yersinia in macrophages triggers receptor-interacting serine/threonine-protein kinase 1 (RIPK1)-dependent caspase-8 cleavage of gasdermin D (GSDMD) and inflammatory cell death (pyroptosis). A genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen to uncover mediators of caspase-8-dependent pyroptosis identified an unexpected role of the lysosomal FLCN-FNIP2-Rag-Ragulator supercomplex, which regulates metabolic signalling and the mechanistic target of rapamycin complex 1 (mTORC1). In response to Yersinia infection, FADD, RIPK1 and caspase-8 were recruited to Rag-Ragulator, causing RIPK1 phosphorylation and caspase-8 activation. Pyroptosis activation depended on Rag GTPase activity and lysosomal tethering of Rag-Ragulator, but not mTORC1. Thus, the lysosomal metabolic regulator Rag-Ragulator instructs the inflammatory response to Yersinia.

DOI: https://doi.org/10.1126/science.abg0269
Front Endocrinol (Lausanne). 2021 ;12 750261

Adipocyte-Specific Inhibition of Mir221/222 Ameliorates Diet-Induced Obesity Through Targeting Ddit4.

Satoshi Yamaguchi, Dongxiao Zhang, Akihiro Katayama, Naoko Kurooka, Ryosuke Sugawara, Haya Hamed Hassan Albuayjan, Atsuko Nakatsuka, Jun Eguchi, Jun Wada.

  MicroRNAs expressed in adipocytes are involved in transcriptional regulation of target mRNAs in obesity, but miRNAs critically involved in this process is not well characterized. Here, we identified upregulation of miR-221-3p and miR-222-3p in the white adipose tissues in C57BL/6 mice fed with high fat-high sucrose (HFHS) chow by RNA sequencing. Mir221 and Mir222 are paralogous genes and share the common seed sequence and Mir221/222AdipoKO mice fed with HFHS chow demonstrated resistance to the development of obesity compared with Mir221/222flox/y . Ddit4 is a direct target of Mir221 and Mir222, and the upregulation of Ddit4 in Mir221/222AdipoKO was associated with the suppression of TSC2 (tuberous sclerosis complex 2)/mammalian target of rapamycin complex 1 (mTORC1)/S6K (ribosomal protein S6 kinase) pathway. The overexpression of miR-222-3p linked to enhanced adipogenesis, and it may be a potential candidate for miRNA-based therapy.

Keywords:  Adipogenesis; adipose tissues; mTORC1; microRNA; non-coding RNAs

DOI:  https://doi.org/10.3389/fendo.2021.750261
J Clin Invest. 2022 Jan 18. pii: e156119. [Epub ahead of print]132(2):

Sensing of RNA stress by mTORC1 drives autoinflammation.

Min Ae Lee-Kirsch.

Loss-of-function mutations in SKIV2L underlie trichohepatoenteric syndrome (THES2), a rare inborn error of immunity characterized by diarrhea, skin lesions, brittle hair, and immunodeficiency. SKIV2L is part of a multiprotein complex required for exosome-mediated RNA surveillance through RNA decay. In this issue of the JCI, Yang et al. delineate a mechanism underlying autoinflammatory skin disease in Skiv2l-deficient mice. Thus, a lack of SKIV2L activates mTORC1 signaling in keratinocytes and T cells, impeding skin barrier integrity and T cell homeostasis. Interestingly, treatment with the mTOR inhibitor rapamycin improves skin symptoms in Skiv2l-deficient mice, suggesting a possible therapeutic avenue for patients with THES2.

DOI: https://doi.org/10.1172/JCI156119
Trends Pharmacol Sci. 2022 Jan 15. pii: S0165-6147(21)00232-7. [Epub ahead of print]

Progranulin as a therapeutic target in neurodegenerative diseases.

Herve Rhinn, Nadine Tatton, Stella McCaughey, Michael Kurnellas, Arnon Rosenthal.

  Progranulin (PGRN, encoded by the GRN gene) plays a key role in the development, survival, function, and maintenance of neurons and microglia in the mammalian brain. It regulates lysosomal biogenesis, inflammation, repair, stress response, and aging. GRN loss-of-function mutations cause neuronal ceroid lipofuscinosis or frontotemporal dementia-GRN (FTD-GRN) in a gene dosage-dependent manner. Mutations that reduce PGRN levels increase the risk for developing Alzheimer's disease, Parkinson's disease, and limbic-predominant age-related transactivation response DNA-binding protein 43 encephalopathy, as well as exacerbate the progression of amyotrophic lateral sclerosis (ALS) and FTD caused by the hexanucleotide repeat expansion in the C9orf72 gene. Elevating and/or restoring PGRN levels is an attractive therapeutic strategy and is being investigated for neurodegenerative diseases through multiple mechanisms of action.

Keywords:  AL001; GRN; frontotemporal dementia; loss of function; neurodegenerative disorders; progranulin

DOI:  https://doi.org/10.1016/j.tips.2021.11.015
Nat Struct Mol Biol. 2022 Jan;29(1): 67-77

ARF GTPases activate Salmonella effector SopF to ADP-ribosylate host V-ATPase and inhibit endomembrane damage-induced autophagy.

Yue Xu, Sen Cheng, Huan Zeng, Ping Zhou, Yan Ma, Lin Li, Xiaoyun Liu, Feng Shao, Jingjin Ding.

Selective autophagy helps eukaryotes to cope with endogenous dangers or foreign invaders; its initiation often involves membrane damage. By studying a Salmonella effector SopF, we recently identified the vacuolar ATPase (V-ATPase)-ATG16L1 axis that initiates bacteria-induced autophagy. Here we show that SopF is an ADP-ribosyltransferase specifically modifying Gln124 of ATP6V0C in V-ATPase. We identify GTP-bound ADP-ribosylation factor (ARF) GTPases as a cofactor required for SopF functioning. Crystal structures of SopF-ARF1 complexes not only reveal structural basis of SopF ADP-ribosyltransferase activity but also a unique effector-binding mode adopted by ARF GTPases. Further, the N terminus of ARF1, although dispensable for high-affinity binding to SopF, is critical for activating SopF to modify ATP6V0C. Moreover, lysosome or Golgi damage-induced autophagic LC3 activation is inhibited by SopF or Q124A mutation of ATP6V0C, thus also mediated by the V-ATPase-ATG16L1 axis. In this process, the V-ATPase functions to sense membrane damages, which can be uncoupled from its proton-pumping activity.

DOI: https://doi.org/10.1038/s41594-021-00710-6
Cells. 2022 Jan 13. pii: 258. [Epub ahead of print]11(2):

Tfeb-Mediated Transcriptional Regulation of Autophagy Induces Autosis during Ischemia/Reperfusion in the Heart.

Jihoon Nah, Eun-Ah Sung, Peiyong Zhai, Daniela Zablocki, Junichi Sadoshima.

  Autosis is a unique form of cell death with characteristic morphological and biochemical features caused by dysregulated autophagy. Autosis is observed in the heart during the late phase of ischemia/reperfusion (I/R), when marked accumulation of autophagosomes is induced. We previously showed that the excessive accumulation of autophagosomes promotes autosis in cardiomyocytes. Although the inhibition of autophagic flux via the upregulation of Rubicon induces the accumulation of autophagosomes during I/R, it appears that additional mechanisms exacerbating autophagosome accumulation are required for the induction of autosis. Here, we show that Tfeb contributes to the induction of autosis during the late phase of I/R in the heart. During myocardial reperfusion, Tfeb is activated and translocated into the nucleus, which in turn upregulates genes involved in autophagy and lysosomal function. The overexpression of Tfeb enhanced cardiomyocyte death induced by a high dose of TAT-Beclin 1, an effect that was inhibited by the downregulation of Atg7. Conversely, the knockdown of Tfeb attenuated high-dose TAT-Beclin1-induced death in cardiomyocytes. Although the downregulation of Tfeb in the heart significantly decreased the number of autophagic vacuoles and inhibited autosis during I/R, the activation of Tfeb activity via 3,4-dimethoxychalcone, an activator of Tfeb, aggravated myocardial injury during I/R. These findings suggest that Tfeb promotes cardiomyocyte autosis during the late phase of reperfusion in the heart.

Keywords:  Tfeb; autophagic cell death; autosis; ischemia/reperfusion

DOI:  https://doi.org/10.3390/cells11020258
Rheumatology (Oxford). 2022 Jan 18. pii: keac037. [Epub ahead of print]

Renal mTORC1 activation is associated with disease activity and prognosis in lupus nephritis.

Zhaomin Mao, Ying Tan, Juan Tao, Linlin Li, Hui Wang, Feng Yu, Andras Perl, Minghui Zhao.

   OBJECTIVE: This study was initiated to evaluate mammalian target of rapamycin (mTOR) activation in renal tissue of lupus nephritis (LN) patients.
METHODS: This retrospective study included 187 LN patients, 20 diabetic nephropathy (DN) patients, 10 minimal change disease (MCD) patients, and 10 normal controls (NCs). 7 of 187 LN patients had repeated renal biopsies. mTORC1/2 activation was evaluated by immunohistochemistry and multiplexed immunofluorescence. The association of mTORC1/2 activation with the clinicopathologic indices and prognostic outcomes was analysed among 187 LN patients. Proteomics was performed in renal biopsies of 20 LN patients. Proteomics was employed to comprehensively evaluate the impact of mTOR activation on intrarenal gene expression.
RESULTS: mTORC1/2 was significantly activated in podocytes, mesangial cells, endothelial cells and tubular epithelial cells of LN patients as compared with those with MCD or NC. The glomerular mTORC1 activation was higher in LN patients compared with DN patients. mTORC1, but not mTORC2, activation strongly correlated with serum albumin, complement C3, proteinuria, and the following pathological biomarkers of LN: crescent formation, interstitial inflammation and fibrosis. Moreover, mTORC1 activation was identified as a prognostic marker in LN patients. Bioinformatic analyses of proteomics and immunohistochemical data unveiled increased complement activation, antigen presentation, and phagocytosis in LN patients with mTORC1 activation.
CONCLUSION: Renal mTORC1 activation could be a biomarker to reveal disease activity and predict clinical prognosis in LN patients.

Keywords:  bioinformatics; lupus nephritis; mTOR; proteomics; rapamycin

DOI:  https://doi.org/10.1093/rheumatology/keac037
Cerebellum. 2022 Jan 18.

The Cerebellum in Niemann-Pick C1 Disease: Mouse Versus Man.

Maria Teresa Fiorenza, Piergiorgio La Rosa, Sonia Canterini, Robert P Erickson.

  Selective neuronal vulnerability is common to most degenerative disorders, including Niemann-Pick C (NPC), a rare genetic disease with altered intracellular trafficking of cholesterol. Purkinje cell dysfunction and loss are responsible for cerebellar ataxia, which is among the prevailing neurological signs of the NPC disease. In this review, we focus on some questions that are still unresolved. First, we frame the cerebellar vulnerability in the context of the extended postnatal time length by which the development of this structure is completed in mammals. In line with this thought, the much later development of cerebellar symptoms in humans is due to the later development and/or maturation of the cerebellum. Hence, the occurrence of developmental events under a protracted condition of defective intracellular cholesterol mobilization hits the functional maturation of the various cell types generating the ground of increased vulnerability. This is particularly consistent with the high cholesterol demand required for cell proliferation, migration, differentiation, and synapse formation/remodeling. Other major questions we address are why the progression of Purkinje cells loss is always from the anterior to the posterior lobes and why cerebellar defects persist in the mouse model even when genetic manipulations can lead to nearly normal survival.

Keywords:  Cholesterol; Development; Lysosomal storage disease; Neuronal differentiation

DOI:  https://doi.org/10.1007/s12311-021-01347-3
Stem Cell Reports. 2022 Jan 03. pii: S2213-6711(21)00652-4. [Epub ahead of print]

Selective elimination of pluripotent stem cells by PIKfyve specific inhibitors.

Arup R Chakraborty, Alex Vassilev, Sushil K Jaiswal, Constandina E O'Connell, John F Ahrens, Barbara S Mallon, Martin F Pera, Melvin L DePamphilis.

  Inhibition of PIKfyve phosphoinositide kinase selectively kills autophagy-dependent cancer cells by disrupting lysosome homeostasis. Here, we show that PIKfyve inhibitors can also selectively eliminate pluripotent embryonal carcinoma cells (ECCs), embryonic stem cells, and induced pluripotent stem cells under conditions where differentiated cells remain viable. PIKfyve inhibitors prevented lysosome fission, induced autophagosome accumulation, and reduced cell proliferation in both pluripotent and differentiated cells, but they induced death only in pluripotent cells. The ability of PIKfyve inhibitors to distinguish between pluripotent and differentiated cells was confirmed with xenografts derived from ECCs. Pretreatment of ECCs with the PIKfyve specific inhibitor WX8 suppressed their ability to form teratocarcinomas in mice, and intraperitoneal injections of WX8 into mice harboring teratocarcinoma xenografts selectively eliminated pluripotent cells. Differentiated cells continued to proliferate, but at a reduced rate. These results provide a proof of principle that PIKfyve specific inhibitors can selectively eliminate pluripotent stem cells in vivo as well as in vitro.

Keywords:  autophagosome; autophagy; cancer stem cells; embryonal carcinoma stem cells; embryonic stem cells; induced pluripotent stem cells; lysosome

DOI:  https://doi.org/10.1016/j.stemcr.2021.12.013
Front Physiol. 2021 ;12 787521

Selective Deletion of the Mechanistic Target of Rapamycin From the Renal Collecting Duct Principal Cell in Mice Down-Regulates the Epithelial Sodium Channel.

Bruce Chen, Maurice B Fluitt, Aaron L Brown, Samantha Scott, Anirudh Gadicherla, Carolyn M Ecelbarger.

  The mechanistic target of rapamycin (mTOR), a serine-threonine-specific kinase, is a cellular energy sensor, integrating growth factor and nutrient signaling. In the collecting duct (CD) of the kidney, the epithelial sodium channel (ENaC) essential in the determination of final urine Na+ losses, has been demonstrated to be upregulated by mTOR, using cell culture and mTOR inhibition in ex vivo preparations. We tested whether CD-principal cell (PC) targeted deletion of mTOR using Cre-lox recombination would affect whole-body sodium homeostasis, blood pressure, and ENaC regulation in mice. Male and female CD-PC mTOR knockout (KO) mice and wild-type (WT) littermates (Cre-negative) were generated using aquaporin-2 (AQP2) promoter to drive Cre-recombinase. Under basal conditions, KO mice showed a reduced (∼30%) natriuretic response to benzamil (ENaC) antagonist, suggesting reduced in vivo ENaC activity. WT and KO mice were fed normal sodium (NS, 0.45% Na+) or a very low Na+ (LS, <0.02%) diet for 7-days. Switching from NS to LS resulted in significantly higher urine sodium losses (relative to WT) in the KO with adaptation occurring by day 2. Blood pressures were modestly (∼5-10 mm Hg) but significantly lower in KO mice under both diets. Western blotting showed KO mice had 20-40% reduced protein levels of all three subunits of ENaC under LS or NS diet. Immunohistochemistry (IHC) of kidney showed enhanced apical-vs.-cellular localization of all three subunits with LS, but a reduction in this ratio for γ-ENaC in the KO. Furthermore, the KO kidneys showed increased ubiquitination of α-ENaC and reduced phosphorylation of the serum and glucocorticoid regulated kinase, type 1 [serum glucocorticoid regulated kinase (SGK1)] on serine 422 (mTOR phosphorylation site). Taken together this suggests enhanced degradation as a consequence of reduced mTOR kinase activity and downstream upregulation of ubiquitination may have accounted for the reduction at least in α-ENaC. Overall, our data support a role for mTOR in ENaC activity likely via regulation of SGK1, ubiquitination, ENaC channel turnover and apical membrane residency. These data support a role for mTOR in the collecting duct in the maintenance of body sodium homeostasis.

Keywords:  insulin; kidney; salt; sex differences; ubiquitination

DOI:  https://doi.org/10.3389/fphys.2021.787521
Allergy. 2022 Jan 17.

TFEB signaling attenuates NLRP3-driven inflammatory responses in severe asthma.

Efthymia Theofani, Maria Semitekolou, Konstantinos Samitas, Annie Mais, Ioanna E Galani, Vasiliki Triantafyllia, Joanna Lama, Ioannis Morianos, Athanasios Stavropoulos, Se-Jin Jeong, Evangelos Andreakos, Babak Razani, Nikoletta Rovina, Georgina Xanthou.

   BACKGROUND: NLRP3-driven inflammatory responses by circulating and lung-resident monocytes are critical drivers of asthma pathogenesis. Autophagy restrains NLRP3-induced monocyte activation in asthma models. Yet, the effects of autophagy and its master regulator, transcription factor EB (TFEB), on monocyte responses in human asthma remain unexplored. Here, we investigated whether activation of autophagy and TFEB signaling suppress inflammatory monocyte responses in asthmatic individuals.
METHODS: Peripheral blood CD14+ monocytes from asthmatic patients (n=83) and healthy controls (n=46) were stimulated with LPS/ATP to induce NLRP3 activation with or without the autophagy inducer, rapamycin. ASC specks, caspase-1 activation, IL-1β and IL-18 levels, mitochondrial function, ROS release and mTORC1 signaling were examined. Autophagy was evaluated by LC3 puncta formation, p62/SQSTM1 degradation and TFEB activation. In a severe asthma (SA) model, we investigated the role of NLRP3 signaling using Nlrp3-/- mice and/or MCC950 administration, and the effects of TFEB activation using myeloid-specific TFEB-overexpressing mice or administration of the TFEB activator, trehalose.
RESULTS: We observed increased NLRP3 inflammasome activation, concomitant with impaired autophagy in circulating monocytes that correlated with asthma severity. SA patients also exhibited mitochondrial dysfunction and ROS accumulation. Autophagy failed to inhibit NLRP3-driven monocyte responses, due to defective TFEB activation and excessive mTORC1 signaling. NLRP3 blockade restrained inflammatory cytokine release and linked airway disease. TFEB activation restored impaired autophagy, attenuated NLRP3-driven pulmonary inflammation and ameliorated SA phenotype.
CONCLUSIONS: Our studies uncover a crucial role for TFEB-mediated reprogramming of monocyte inflammatory responses, raising the prospect that this pathway can be therapeutically harnessed for the management of SA.

Keywords:  NLRP3; TFEB; asthma; autophagy; monocytes

DOI:  https://doi.org/10.1111/all.15221
J Cancer Prev. 2021 Dec 30. 26(4): 237-243

Role of Branched-chain Amino Acid Metabolism in Tumor Development and Progression.

Min Kyu Jung, Akinkunmi Paul Okekunle, Jung Eun Lee, Mi Kyung Sung, Yun Jeong Lim.

  Branched-chain amino acids (BCAAs), isoleucine, leucine and valine, are essential amino acids with vital roles in protein synthesis and energy production. We reviewed the fundamentals of BCAA metabolism in advanced cancer patients. BCAAs and various catabolic products act as signalling molecules, which activate mechanisms ranging from protein synthesis to insulin secretion. Recently, BCAA metabolism has been suggested to contribute to cancer progression. Of particular interest is the modulation of the mTOR activity by BCAAs. There are likely multiple pathways involved in BCAA metabolism implicated in carcinogenesis. Understanding the mechanism(s) underlying altered BCAAs metabolism will significantly advance the current understanding of nutrient involvement in carcinogenesis and direct future studies to unravel the significance of BCCA metabolites in tumor development and progression.

Keywords:  Amino acids; Isoleucine; Leucine; Neoplasm; Valine; branched-chain

DOI:  https://doi.org/10.15430/JCP.2021.26.4.237
J Cell Biol. 2022 Mar 07. pii: e202106124. [Epub ahead of print]221(3):

An endosome-associated actin network involved in directed apical plasma membrane growth.

Luis Daniel Ríos-Barrera, Maria Leptin.

Membrane trafficking plays many roles in morphogenesis, from bulk membrane provision to targeted delivery of proteins and other cargos. In tracheal terminal cells of the Drosophila respiratory system, transport through late endosomes balances membrane delivery between the basal plasma membrane and the apical membrane, which forms a subcellular tube, but it has been unclear how the direction of growth of the subcellular tube with the overall cell growth is coordinated. We show here that endosomes also organize F-actin. Actin assembles around late endocytic vesicles in the growth cone of the cell, reaching from the tip of the subcellular tube to the leading filopodia of the basal membrane. Preventing nucleation of endosomal actin disturbs the directionality of tube growth, uncoupling it from the direction of cell elongation. Severing actin in this area affects tube integrity. Our findings show a new role for late endosomes in directing morphogenesis by organizing actin, in addition to their known role in membrane and protein trafficking.

DOI: https://doi.org/10.1083/jcb.202106124
Pathogens. 2021 Dec 22. pii: 5. [Epub ahead of print]11(1):

Amino Acid Sensing and Assimilation by the Fungal Pathogen Candida albicans in the Human Host.

Fitz Gerald S Silao, Per O Ljungdahl.

  Nutrient uptake is essential for cellular life and the capacity to perceive extracellular nutrients is critical for coordinating their uptake and metabolism. Commensal fungal pathogens, e.g., Candida albicans, have evolved in close association with human hosts and are well-adapted to using diverse nutrients found in discrete host niches. Human cells that cannot synthesize all amino acids require the uptake of the "essential amino acids" to remain viable. Consistently, high levels of amino acids circulate in the blood. Host proteins are rich sources of amino acids but their use depends on proteases to cleave them into smaller peptides and free amino acids. C. albicans responds to extracellular amino acids by pleiotropically enhancing their uptake and derive energy from their catabolism to power opportunistic virulent growth. Studies using Saccharomyces cerevisiae have established paradigms to understand metabolic processes in C. albicans; however, fundamental differences exist. The advent of CRISPR/Cas9-based methods facilitate genetic analysis in C. albicans, and state-of-the-art molecular biological techniques are being applied to directly examine growth requirements in vivo and in situ in infected hosts. The combination of divergent approaches can illuminate the biological roles of individual cellular components. Here we discuss recent findings regarding nutrient sensing with a focus on amino acid uptake and metabolism, processes that underlie the virulence of C. albicans.

Keywords:  Candida albicans; SPS-sensor; amino acid metabolism; glucose repression; human fungal pathogen; mitochondria; nitrogen catabolite repression; nutrient sensing; proline catabolism

DOI:  https://doi.org/10.3390/pathogens11010005
Elife. 2022 Jan 18. pii: e69709. [Epub ahead of print]11

Lipid kinases VPS34 and PIKfyve coordinate a phosphoinositide cascade to regulate Retriever-mediated recycling on endosomes.

Sai Srinivas Panapakkam Giridharan, Guangming Luo, Pilar Rivero-Rios, Noah Steinfeld, Helene Tronchere, Amika Singla, Ezra Burstein, Daniel D Billadeau, Michael A Sutton, Lois S Weisman.

  Cell-surface receptors control how cells respond to their environment. Many cell-surface receptors recycle from endosomes to the plasma membrane via a recently discovered pathway, which includes sorting-nexin SNX17, Retriever, WASH and CCC complexes. Here, using mammalian cells, we discover that PIKfyve and its upstream PI3-kinase VPS34 positively regulate this pathway. VPS34 produces PI3P, which is the substrate for PIKfyve to generate PI3,5P2. We show that PIKfyve controls recycling of cargoes including integrins, receptors that control cell migration. Furthermore, endogenous PIKfyve colocalizes with SNX17, Retriever, WASH and CCC complexes on endosomes. Importantly, PIKfyve inhibition results displacement of Retriever and CCC from endosomes. In addition, we show that recruitment of SNX17 is an early step and requires VPS34. These discoveries suggest that VPS34 and PIKfyve coordinate an ordered pathway to regulate recycling from endosomes and suggest how PIKfyve functions in cell migration.

Keywords:  cell biology

DOI:  https://doi.org/10.7554/eLife.69709
Nat Immunol. 2022 Jan 20.

mTORC2 forms iron-clad defense to guard memory.

Jordy Saravia, Hongbo Chi.

DOI: https://doi.org/10.1038/s41590-021-01100-2
Cell. 2022 Jan 14. pii: S0092-8674(21)01563-4. [Epub ahead of print]

Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.

Tara E Tracy, Jesus Madero-Pérez, Danielle L Swaney, Timothy S Chang, Michelle Moritz, Csaba Konrad, Michael E Ward, Erica Stevenson, Ruth Hüttenhain, Grant Kauwe, Maria Mercedes, Lauren Sweetland-Martin, Xu Chen, Sue-Ann Mok, Man Ying Wong, Maria Telpoukhovskaia, Sang-Won Min, Chao Wang, Peter Dongmin Sohn, Jordie Martin, Yungui Zhou, Wenjie Luo, John Q Trojanowski, Virginia M Y Lee, Shiaoching Gong, Giovanni Manfredi, Giovanni Coppola, Nevan J Krogan, Daniel H Geschwind, Li Gan.

  Tau (MAPT) drives neuronal dysfunction in Alzheimer disease (AD) and other tauopathies. To dissect the underlying mechanisms, we combined an engineered ascorbic acid peroxidase (APEX) approach with quantitative affinity purification mass spectrometry (AP-MS) followed by proximity ligation assay (PLA) to characterize Tau interactomes modified by neuronal activity and mutations that cause frontotemporal dementia (FTD) in human induced pluripotent stem cell (iPSC)-derived neurons. We established interactions of Tau with presynaptic vesicle proteins during activity-dependent Tau secretion and mapped the Tau-binding sites to the cytosolic domains of integral synaptic vesicle proteins. We showed that FTD mutations impair bioenergetics and markedly diminished Tau's interaction with mitochondria proteins, which were downregulated in AD brains of multiple cohorts and correlated with disease severity. These multimodal and dynamic Tau interactomes with exquisite spatial resolution shed light on Tau's role in neuronal function and disease and highlight potential therapeutic targets to block Tau-mediated pathogenesis.

Keywords:  APEX; Tau; Tau secretion; affinity purification mass spectrometry; interactome; mitochondria; neurodegeneration; protein-protein interaction; synapse; tauopathies

DOI:  https://doi.org/10.1016/j.cell.2021.12.041
Nature. 2022 Jan 19.

Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis.

Kevin C Stein, Fabián Morales-Polanco, Joris van der Lienden, T Kelly Rainbolt, Judith Frydman.

Ageing is accompanied by a decline in cellular proteostasis, which underlies many age-related protein misfolding diseases1,2. Yet, how ageing impairs proteostasis remains unclear. As nascent polypeptides represent a substantial burden on the proteostasis network3, we hypothesized that altered translational efficiency during ageing could help to drive the collapse of proteostasis. Here we show that ageing alters the kinetics of translation elongation in both Caenorhabditis elegans and Saccharomyces cerevisiae. Ribosome pausing was exacerbated at specific positions in aged yeast and worms, including polybasic stretches, leading to increased ribosome collisions known to trigger ribosome-associated quality control (RQC)4-6. Notably, aged yeast cells exhibited impaired clearance and increased aggregation of RQC substrates, indicating that ageing overwhelms this pathway. Indeed, long-lived yeast mutants reduced age-dependent ribosome pausing, and extended lifespan correlated with greater flux through the RQC pathway. Further linking altered translation to proteostasis collapse, we found that nascent polypeptides exhibiting age-dependent ribosome pausing in C. elegans were strongly enriched among age-dependent protein aggregates. Notably, ageing increased the pausing and aggregation of many components of proteostasis, which could initiate a cycle of proteostasis collapse. We propose that increased ribosome pausing, leading to RQC overload and nascent polypeptide aggregation, critically contributes to proteostasis impairment and systemic decline during ageing.

DOI: https://doi.org/10.1038/s41586-021-04295-4
J Clin Invest. 2022 Jan 18. pii: e146176. [Epub ahead of print]132(2):

Cytoplasmic RNA quality control failure engages mTORC1-mediated autoinflammatory disease.

Kun Yang, Jie Han, Mayumi Asada, Jennifer G Gill, Jason Y Park, Meghana N Sathe, Jyothsna Gattineni, Tracey Wright, Christian A Wysocki, M Teresa de la Morena, Luis A Garza, Nan Yan.

  Inborn errors of nucleic acid metabolism often cause aberrant activation of nucleic acid sensing pathways, leading to autoimmune or autoinflammatory diseases. The SKIV2L RNA exosome is cytoplasmic RNA degradation machinery that was thought to be essential for preventing the self-RNA-mediated interferon (IFN) response. Here, we demonstrate the physiological function of SKIV2L in mammals. We found that Skiv2l deficiency in mice disrupted epidermal and T cell homeostasis in a cell-intrinsic manner independently of IFN. Skiv2l-deficient mice developed skin inflammation and hair abnormality, which were also observed in a SKIV2L-deficient patient. Epidermis-specific deletion of Skiv2l caused hyperproliferation of keratinocytes and disrupted epidermal stratification, leading to impaired skin barrier with no appreciable IFN activation. Moreover, Skiv2l-deficient T cells were chronically hyperactivated and these T cells attacked lesional skin as well as hair follicles. Mechanistically, SKIV2L loss activated the mTORC1 pathway in both keratinocytes and T cells. Both systemic and topical rapamycin treatment of Skiv2l-deficient mice ameliorated epidermal hyperplasia and skin inflammation. Together, we demonstrate that mTORC1, a classical nutrient sensor, also senses cytoplasmic RNA quality control failure and drives autoinflammatory disease. We also propose SKIV2L-associated trichohepatoenteric syndrome (THES) as a new mTORopathy for which sirolimus may be a promising therapy.

Keywords:  Autoimmune diseases; Autoimmunity; Genetic diseases; Metabolism; Skin

DOI:  https://doi.org/10.1172/JCI146176
Cells. 2022 Jan 06. pii: 190. [Epub ahead of print]11(2):

Nephropathic Cystinosis: Pathogenic Roles of Inflammation and Potential for New Therapies.

Mohamed A Elmonem, Koenraad R P Veys, Giusi Prencipe.

  The activation of several inflammatory pathways has recently been documented in patients and different cellular and animal models of nephropathic cystinosis. Upregulated inflammatory signals interact with many pathogenic aspects of the disease, such as enhanced oxidative stress, abnormal autophagy, inflammatory cell recruitment, enhanced cell death, and tissue fibrosis. Cysteamine, the only approved specific therapy for cystinosis, ameliorates many but not all pathogenic aspects of the disease. In the current review, we summarize the inflammatory mechanisms involved in cystinosis and their potential impact on the disease pathogenesis and progression. We further elaborate on the crosstalk between inflammation, autophagy, and apoptosis, and discuss the potential of experimental drugs for suppressing the inflammatory signals in cystinosis.

Keywords:  apoptosis; autophagy; chitotriosidase; cysteamine; endocytosis; galectin-3; inflammasome; interleukins; macrophages; novel therapies; proximal tubular cells

DOI:  https://doi.org/10.3390/cells11020190
Nat Nanotechnol. 2022 Jan 17.

Subcutaneous nanotherapy repurposes the immunosuppressive mechanism of rapamycin to enhance allogeneic islet graft viability.

Jacqueline A Burke, Xiaomin Zhang, Sharan Bobbala, Molly A Frey, Carolina Bohorquez Fuentes, Helena Freire Haddad, Sean D Allen, Reese A K Richardson, Guillermo A Ameer, Evan A Scott.

Standard oral rapamycin (that is, Rapamune) administration is plagued by poor bioavailability and broad biodistribution. Thus, this pleotropic mammalian target of rapamycin (mTOR) inhibitor has a narrow therapeutic window and numerous side effects and provides inadequate protection to transplanted cells and tissues. Furthermore, the hydrophobicity of rapamycin limits its use in parenteral formulations. Here, we demonstrate that subcutaneous delivery via poly(ethylene glycol)-b-poly(propylene sulfide) polymersome nanocarriers significantly alters rapamycin's cellular biodistribution to repurpose its mechanism of action for tolerance, instead of immunosuppression, and minimize side effects. While oral rapamycin inhibits T cell proliferation directly, subcutaneously administered rapamycin-loaded polymersomes modulate antigen presenting cells in lieu of T cells, significantly improving maintenance of normoglycemia in a clinically relevant, major histocompatibility complex-mismatched, allogeneic, intraportal (liver) islet transplantation model. These results demonstrate the ability of a rationally designed nanocarrier to re-engineer the immunosuppressive mechanism of a drug by controlling cellular biodistribution.

DOI: https://doi.org/10.1038/s41565-021-01048-2
Proc Natl Acad Sci U S A. 2022 Jan 25. pii: e2114622119. [Epub ahead of print]119(4):

Yeast has evolved to minimize protein resource cost for synthesizing amino acids.

Yu Chen, Jens Nielsen.

  Proteins, as essential biomolecules, account for a large fraction of cell mass, and thus the synthesis of the complete set of proteins (i.e., the proteome) represents a substantial part of the cellular resource budget. Therefore, cells might be under selective pressures to optimize the resource costs for protein synthesis, particularly the biosynthesis of the 20 proteinogenic amino acids. Previous studies showed that less energetically costly amino acids are more abundant in the proteomes of bacteria that survive under energy-limited conditions, but the energy cost of synthesizing amino acids was reported to be weakly associated with the amino acid usage in Saccharomyces cerevisiae Here we present a modeling framework to estimate the protein cost of synthesizing each amino acid (i.e., the protein mass required for supporting one unit of amino acid biosynthetic flux) and the glucose cost (i.e., the glucose consumed per amino acid synthesized). We show that the logarithms of the relative abundances of amino acids in S. cerevisiae's proteome correlate well with the protein costs of synthesizing amino acids (Pearson's r = -0.89), which is better than that with the glucose costs (Pearson's r = -0.5). Therefore, we demonstrate that S. cerevisiae tends to minimize protein resource, rather than glucose or energy, for synthesizing amino acids.

Keywords:  Saccharomyces cerevisiae; amino acid biosynthetic cost; constraint-based modeling; metabolic engineering; proteome constraint

DOI:  https://doi.org/10.1073/pnas.2114622119